4HQM

The crystal structure of QsrR-menadione complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.55 Å
  • R-Value Free: 
    0.296 (Depositor), 0.299 (DCC) 
  • R-Value Work: 
    0.284 (Depositor), 0.277 (DCC) 
  • R-Value Observed: 
    0.285 (Depositor) 

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Ligand Structure Quality Assessment 

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This is version 1.2 of the entry. See complete history


Literature

Molecular mechanism of quinone signaling mediated through S-quinonization of a YodB family repressor QsrR.

Ji, Q.Zhang, L.Jones, M.B.Sun, F.Deng, X.Liang, H.Cho, H.Brugarolas, P.Gao, Y.N.Peterson, S.N.Lan, L.Bae, T.He, C.

(2013) Proc Natl Acad Sci U S A 110: 5010-5015

  • DOI: https://doi.org/10.1073/pnas.1219446110
  • Primary Citation of Related Structures:  
    4HQE, 4HQM

  • PubMed Abstract: 

    Quinone molecules are intracellular electron-transport carriers, as well as critical intra- and extracellular signals. However, transcriptional regulation of quinone signaling and its molecular basis are poorly understood. Here, we identify a thiol-stress-sensing regulator YodB family transcriptional regulator as a central component of quinone stress response of Staphylococcus aureus, which we have termed the quinone-sensing and response repressor (QsrR). We also identify and confirm an unprecedented quinone-sensing mechanism based on the S-quinonization of the essential residue Cys-5. Structural characterizations of the QsrR-DNA and QsrR-menadione complexes further reveal that the covalent association of menadione directly leads to the release of QsrR from operator DNA following a 10° rigid-body rotation as well as a 9-Å elongation between the dimeric subunits. The molecular level characterization of this quinone-sensing transcriptional regulator provides critical insights into quinone-mediated gene regulation in human pathogens.


  • Organizational Affiliation

    Department of Chemistry, The University of Chicago, Chicago, IL 60637, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
QsrR protein
A, B
115Staphylococcus aureusMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.55 Å
  • R-Value Free:  0.296 (Depositor), 0.299 (DCC) 
  • R-Value Work:  0.284 (Depositor), 0.277 (DCC) 
  • R-Value Observed: 0.285 (Depositor) 
Space Group: P 6
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 124.758α = 90
b = 124.758β = 90
c = 30.633γ = 120
Software Package:
Software NamePurpose
HKL-2000data collection
PHASESphasing
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

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Ligand Structure Quality Assessment 

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2013-03-06
    Type: Initial release
  • Version 1.1: 2013-05-22
    Changes: Database references
  • Version 1.2: 2024-11-20
    Changes: Data collection, Database references, Derived calculations, Structure summary